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Dense sampling of bird diversity increases power of comparative genomics.

  • Author(s): Feng, Shaohong
  • Stiller, Josefin
  • Deng, Yuan
  • Armstrong, Joel
  • Fang, Qi
  • Reeve, Andrew Hart
  • Xie, Duo
  • Chen, Guangji
  • Guo, Chunxue
  • Faircloth, Brant C
  • Petersen, Bent
  • Wang, Zongji
  • Zhou, Qi
  • Diekhans, Mark
  • Chen, Wanjun
  • Andreu-Sánchez, Sergio
  • Margaryan, Ashot
  • Howard, Jason Travis
  • Parent, Carole
  • Pacheco, George
  • Sinding, Mikkel-Holger S
  • Puetz, Lara
  • Cavill, Emily
  • Ribeiro, Ângela M
  • Eckhart, Leopold
  • Fjeldså, Jon
  • Hosner, Peter A
  • Brumfield, Robb T
  • Christidis, Les
  • Bertelsen, Mads F
  • Sicheritz-Ponten, Thomas
  • Tietze, Dieter Thomas
  • Robertson, Bruce C
  • Song, Gang
  • Borgia, Gerald
  • Claramunt, Santiago
  • Lovette, Irby J
  • Cowen, Saul J
  • Njoroge, Peter
  • Dumbacher, John Philip
  • Ryder, Oliver A
  • Fuchs, Jérôme
  • Bunce, Michael
  • Burt, David W
  • Cracraft, Joel
  • Meng, Guanliang
  • Hackett, Shannon J
  • Ryan, Peter G
  • Jønsson, Knud Andreas
  • Jamieson, Ian G
  • da Fonseca, Rute R
  • Braun, Edward L
  • Houde, Peter
  • Mirarab, Siavash
  • Suh, Alexander
  • Hansson, Bengt
  • Ponnikas, Suvi
  • Sigeman, Hanna
  • Stervander, Martin
  • Frandsen, Paul B
  • van der Zwan, Henriette
  • van der Sluis, Rencia
  • Visser, Carina
  • Balakrishnan, Christopher N
  • Clark, Andrew G
  • Fitzpatrick, John W
  • Bowman, Reed
  • Chen, Nancy
  • Cloutier, Alison
  • Sackton, Timothy B
  • Edwards, Scott V
  • Foote, Dustin J
  • Shakya, Subir B
  • Sheldon, Frederick H
  • Vignal, Alain
  • Soares, André ER
  • Shapiro, Beth
  • González-Solís, Jacob
  • Ferrer-Obiol, Joan
  • Rozas, Julio
  • Riutort, Marta
  • Tigano, Anna
  • Friesen, Vicki
  • Dalén, Love
  • Urrutia, Araxi O
  • Székely, Tamás
  • Liu, Yang
  • Campana, Michael G
  • Corvelo, André
  • Fleischer, Robert C
  • Rutherford, Kim M
  • Gemmell, Neil J
  • Dussex, Nicolas
  • Mouritsen, Henrik
  • Thiele, Nadine
  • Delmore, Kira
  • Liedvogel, Miriam
  • Franke, Andre
  • Hoeppner, Marc P
  • Krone, Oliver
  • Fudickar, Adam M
  • Milá, Borja
  • Ketterson, Ellen D
  • Fidler, Andrew Eric
  • Friis, Guillermo
  • Parody-Merino, Ángela M
  • Battley, Phil F
  • Cox, Murray P
  • Lima, Nicholas Costa Barroso
  • Prosdocimi, Francisco
  • Parchman, Thomas Lee
  • Schlinger, Barney A
  • Loiselle, Bette A
  • Blake, John G
  • Lim, Haw Chuan
  • Day, Lainy B
  • Fuxjager, Matthew J
  • Baldwin, Maude W
  • Braun, Michael J
  • Wirthlin, Morgan
  • Dikow, Rebecca B
  • Ryder, T Brandt
  • Camenisch, Glauco
  • Keller, Lukas F
  • DaCosta, Jeffrey M
  • Hauber, Mark E
  • Louder, Matthew IM
  • Witt, Christopher C
  • McGuire, Jimmy A
  • Mudge, Joann
  • Megna, Libby C
  • Carling, Matthew D
  • Wang, Biao
  • Taylor, Scott A
  • Del-Rio, Glaucia
  • Aleixo, Alexandre
  • Vasconcelos, Ana Tereza Ribeiro
  • Mello, Claudio V
  • Weir, Jason T
  • Haussler, David
  • Li, Qiye
  • Yang, Huanming
  • Wang, Jian
  • Lei, Fumin
  • Rahbek, Carsten
  • Gilbert, M Thomas P
  • Graves, Gary R
  • Jarvis, Erich D
  • Paten, Benedict
  • Zhang, Guojie
  • et al.
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

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